Hello gurus,

I made some slight progress...

If I specify a handlers section into the job_conf.xml file with:
    <handlers>
        <handler id="main"/>
    </handlers>


Then galaxy would at least start.  However, it is not very functional, I
can't upload files or run job, it says:

An error occurred with this dataset:*Unable to run job due to a
misconfiguration of the Galaxy job running system. Please contact a site
administrator.*


My universe_wsgi.conf is fairly stock, the [server:main] section is
certainly there.  The most relevant changes are:
    start_job_runners = drmaa
    default_cluster_job_runner =  drmaa://-q default.q -V -v
TMPDIR=/scratch/


If someone can point me to a job_conf.xml so that I can set the TMPDIR
param correctly for qsub (sge), that would be greatly appreciated!

Thanks
-Tin




On Wed, Aug 14, 2013 at 8:04 AM, Jennifer Jackson <j...@bx.psu.edu> wrote:

>  -------- Original Message --------  Subject: Re: how to add settings of
> TMPDIR=/scratch for sge/drmaa in universe_wsgi.ini  Date: Tue, 13 Aug
> 2013 23:21:16 -0700  From: tin h <tin6...@gmail.com> <tin6...@gmail.com>  To:
> Jennifer Jackson <j...@bx.psu.edu> <j...@bx.psu.edu>  CC: Galaxy Dev
> <galaxy-...@bx.psu.edu> <galaxy-...@bx.psu.edu>
>
>
>
> Thank you Jennifer.
>
>  I am not sure if my previous email got gabled up...
> Just to be sure, I specified the following in universe_wsgi.ini
>      default_cluster_job_runner = drmaa://-q default.q -V -v
> TMPDIR=/scratch/
>
>  when i start galaxy, looking at the console log, this is what I see:
>
>
>  galaxy.jobs DEBUG 2013-08-14 14:08:14,885 Loaded job runner
> 'galaxy.jobs.runners.drmaa:DRMAAJobRunner' as 'drmaa'
> galaxy.jobs.runners.drmaa DEBUG 2013-08-14 14:08:14,885 Converted URL
> 'drmaa://-q default.q -V -v TMPDIR=/scratch/' to destination runner=drmaa,
> params={'nativeSpecification': '-q default.q -V -v TMPDIR='}
> galaxy.jobs DEBUG 2013-08-14 14:08:14,885 Legacy destination with id
> 'drmaa://-q default.q -V -v TMPDIR=/scratch/', url 'drmaa://-q default.q -V
> -v TMPDIR=/scratch/' converted, got params:
> galaxy.jobs DEBUG 2013-08-14 14:08:14,885     nativeSpecification: -q
> default.q -V -v TMPDIR=
>
>
>  The parser has stopped at the / before scratch and ignored the rest :(
>
>
>  I did  refer to
> http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster and tried
> to define job_conf.xml as
>
>  <?xml version="1.0"?>
>   <job_conf>
>     <plugins>
>         <plugin id="local" type="runner"
> load="galaxy.jobs.runners.local:LocalJobRunner" workers="4"/>
>         <plugin id="sge" type="runner"
> load="galaxy.jobs.runners.drmaa:DRMAAJobRunner"/>
>     </plugins>
>     <destinations default="sge_default">
>         <destination id="sge_default" runner="drmaa">
>                 <param id="nativeSpecification">-q default.q -V -v
> TMPDIR=/scratch</param>
>         </destination>
>     </destinations>
> </job_conf>
>
>
>  But then galaxy won't start, giving me the error of:
>
>  Traceback (most recent call last):
>   File
> "/usr/prog/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line
> 37, in app_factory
>     app = UniverseApplication( global_conf = global_conf, **kwargs )
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/app.py", line 95, in
> __init__
>     self.job_config = jobs.JobConfiguration(self)
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
> 107, in __init__
>     self.__parse_job_conf_xml(tree)
>    File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
> 157, in __parse_job_conf_xml
>     self.default_handler_id = self.__get_default(handlers,
> self.handlers.keys())
>   File "/usr/prog/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line
> 286, in __get_default
>     rval = parent.get('default')
> AttributeError: 'NoneType' object has no attribute 'get'
>
>  I am not sure what the "default" refers to, doesn't seems to be the
> destinations default specified as I tried changing that name but the error
> message remains the same.
>
>  Any help so that I can pass TMPDIR=/scratch into SGE qsub would be
> greatly appreciated.
>
>
>  -Tin
>
>
>
>
>  --
>
>  I am riding to fundraise for the Cystic Fibrosis Foundation.  Please
> consider a tax deductible donation at
> http://www.cff.org/LWC/dsp_DonationPage.cfm?idEvent=23815&idUser=615989
>
>
>         ~~~            __o            Engineering is the art of making
> compromises.
>          ~~~         _ <_             Science is the reverse engineering
> of the compromises made by nature.
>        ~~~          (_)/(_)            Medicine is the hacking of the
> scientific knowledge base.   - A comp sci student :-)
>
>  On 8/13/13 7:28 PM, Jennifer Jackson wrote:
>
> Hi Tin,
>
> I am going to move this over to the galaxy-...@bx.psu.edu mailing list
> (good for local install questions) to give it better viability.
>
> I am by no means the best person to help with this, so hopefully others
> will jump in, but just from looking at this I am wondering if you shouldn't
> be instead looking at the " job_conf.xml.sample_advanced" file. There is
> the default version as well, but it is probably not what you are looking
> for if you want to add custom logging scripts.
>
> For universe_wsgi.ini, it seems like maybe the problem with the syntax is
> most likely the unknown "default_cluster_job_runner" variable and the
> double "=" in the line. Slashes should be fine unescaped here. But as I
> said, I think the other file is the place for the changes anyway, or maybe
> both, but using known variables and a single "=" per path.
>
> But let's see what the developers think!
>
> Jen
> Galaxy team
>
> On 8/12/13 3:49 PM, tin h wrote:
>
>
> Hello galaxy gurus,Â
>
>  I am trying to configure a local galaxy server to submit to SGE using
> DRMAA,Â
> it works, but I would like to specify the equivalent of "-v
> TMPDIR=/scratch" for qsub.
>
>  I tried updating universe_wsgi.ini with something like:
>  Â  default_cluster_job_runner = Â drmaa://-q default.q -V -v
> TMPDIR=/scratch/
>  but that doesn't work because "/" is a delimiter, and I have not been
> able to find way to escape it. Â Is there any tricks for this?
>
>
>  Much thanks in advance for your help in this matter.
> -Tin
>
>
> ___________________________________________________________
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> --
> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>
>
>
> ___________________________________________________________
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> --
> Jennifer Hillman-Jacksonhttp://galaxyproject.org
>
>
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